copynumberConversion {beadarraySNP} | R Documentation

## Conversion to Copynumber analysis objects

### Description

SnpSetIllumina objects are converted to other objects for numerical analysis

### Usage

      convert2aCGH(object,normalizedTo=2,doLog=TRUE,organism="hsa")
      convert2SegList(object,normalizedTo=2,doLog=TRUE,organism="hsa")

### Arguments

`object` | SnpSetIllumina object
`normalizedTo` | numeric, 'normal' copynumber datavalue for object
`doLog` | logical, perform logarithmic transformation (log2)
`organism` | character, organism used in object. Currently 'hsa' and 'mmu' are recognized. Used to convert sex chromosomes to their proper numerical representation

### Details

These functions produce objects that can be used by the analysis functions in the aCGH or snapCGH packages. The SnpSetIllumina intensity values are stored in a linear scale. Both types of objects assume a logarithmic scale, so by default the values are transformed to a log2 scale centered around 0.

### Value

`convert2aCGH` returns a `aCGH` object as used in the aCGH package. `convert2SegList` returns a `SegList` object as used in the snapCGH package.

### Author(s)

Jan Oosting

### See Also

`SnpSetIllumina-class`, `aCGH-class`, `SegList-class`

[Package beadarraySNP version 1.60.0 Index]